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Home modified by Willem Jan Palenstijn

Willem Jan Palenstijn — Mon, 24 Oct 2016 16:07:10 -0000

--- v23
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-# ASTRA Tomography Toolbox documentation
-
-## News
-
-* 2015-12-23: New version **1.7.1beta** released. This is a small bugfix release after v1.7beta. ASTRA version 1.7beta contains a few large experimental new features, which is why we have given it the beta tag.
-If it does not work properly for you, all files for astra-1.6 are also still available for download: astra-1.6 downloads. New features:
-    * Experimental MPI distributed computing support in Python. This is only available for Linux+Python, as a separate source download (astra-1.7.1beta_MPI.tar. bz2), or the mpi branch on github.
-    * Experimental support in Python for FP and BP of objects composited from multiple 3d data objects, at possibly different resolutions. This also removes some restrictions on data size for 3D GPU FP and BP.
-    * Reduced restrictions on volume geometries: The volume no longer has to be centered, and voxels still have to be cubes, but no longer 1x1x1.
-
-
-* 2015-05-29: New version **1.6** released. The Python interface developed by Daniel Pelt, and the Matlab Spot toolbox operator wrapping ASTRA developed by Folkert Bleichrodt are now integrated into the main ASTRA Toolbox source tree.
-
-* 2015-01-17: From 25 to 27 March, 2015, iMinds-Vision Lab organizes the second ASTRA Toolbox training session. For more info, please contact Wim Van Aarle: wim.vanaarle@uantwerpen.be.
-
-* 2014-02-25: From 9 to 11 April 2014, the iMinds-Vision Lab organizes a training session entitled "Unleashing the ASTRA Tomography Toolbox".
-
-* 2013-07-12: Folkert Bleichrodt from CWI has contributed a wrapper around the ASTRA Toolbox for the Spot toolbox.
-
-* 2013-07-02: New version 1.3 released with some bug fixes and including a version of the DART algorithm by Wim van Aarle from the Vision Lab at the University of Antwerp.
-
-* 2013-04-24: Daniël M. Pelt from CWI has released a Python interface for the ASTRA Toolbox.
-
-* 2012-08-20: ASTRA Toolbox, developed by iMinds-Vision Lab of the University of Antwerp, launched!
-
-## [Introduction]
-
-## [Sample scripts]
-
-## Downloads
-
-Main downloads:
-
-* ASTRA v1.7.1beta for Windows 64 bit CUDA/MATLAB: [astra-1.7.1beta-matlab-win-x64.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta-matlab-win-x64.zip/download)
-
-* ASTRA v1.7.1beta for Windows 64 bit CUDA/Python 2.7: [astra-1.7.1beta-python27-win-x64.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta-python27-win-x64.zip/download)
-
-* ASTRA v1.7.1beta for Windows 64 bit CUDA/Python 3.4: [astra-1.7.1beta-python34-win-x64.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta-python34-win-x64.zip/download)
-
-* ASTRA v1.7.1beta Source Code for Linux: [astra-1.7.1beta.tar.bz2](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta.tar.bz2/download)
-
-* ASTRA v1.7.1beta Source Code for Linux, with MPI support: [astra-1.7.1beta_MPI.tar.bz2](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta_MPI.tar.bz2/download)
-
-For compiling on Windows we only provide Visual Studio 2008 and 2012 project files. We have also packaged a set of external libraries and headers for all the build dependencies:
-
-* ASTRA v1.7.1beta Source Code for Windows/VS2008/2012: [astra-1.7.1beta.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta.zip/download)
-* ASTRA v1.7.1beta Compilation Support files for Windows/VS2008/2012: [astra-1.7.1beta-windows_build_support.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta-windows_build_support.zip/download)
-
-
-
-## Reference guide
-
-Geometries:
-
-* [2D Geometries]
-  volume, parallel, fanflat, fanflat_vec, sparse_matrix 
-* [3D Geometries]
-  volume, parallel3d, cone, parallel3d_vec, cone_vec 
-* [astra_create_proj_geom]
-* [astra_create_vol_geom]
-
-Projectors:
-
-* [2D Projectors]
-  line, strip, linear, line_fanflat, strip_fanflat, sparse_matrix, cuda 
-* [astra_create_projector]
-* [astra_mex_projector]
-
-Data objects:
-
-* [astra_mex_data2d]
-* [astra_mex_data3d]
-
-Algorithms:
-
-* [astra_mex_algorithm]
-* [2D CPU Algorithms]
-  [FP], [BP], [FBP], [SIRT], [SART], [ART], [CGLS]
-* [2D GPU Algorithms]
-  [FP_CUDA], [BP_CUDA], [FBP_CUDA], [SIRT_CUDA], [SART_CUDA], [CGLS_CUDA], [EM_CUDA]
-* [3D GPU Algorithms]
-  [FP3D_CUDA], [BP3D_CUDA]], [FDK_CUDA], [SIRT3D_CUDA], [CGLS3D_CUDA]
-* [Masks]
-
-Miscellaneous:
-
-* [astra_struct]
-* [astra_mex_matrix]
-
-[ASTRA utility scripts]
-
-* astra_create_sino
-* astra_create_backprojection
-* astra_create_sino_cuda
-* astra_create_backprojection_cuda
-* astra_create_sino3d_cuda
-* astra_create_backprojection3d_cuda
-* astra_geom_2vec
-* astra_geom_size
+# The ASTRA Tomography Toolbox is now hosted at http://www.astra-toolbox.com/

Discussion for Home page

Willem Jan Palenstijn — Fri, 15 Apr 2016 09:10:47 -0000

Hi,

Thank you for your interest in astra, but please contact us directly via email at astra@uantwerpen.be. (This is not really a discussion forum.)

The script you're trying, test_dart.m, does not run SIRT3D_CUDA, but it runs the discrete tomography DART algorithm, which requires samples with specific properties and a significant amount of setting of parameters to get usable results. For SIRT3D_CUDA reconstructions, I would recommend starting from the s007_3d_reconstruction.m sample script.

To keep this front page clean, I will delete these posts again next week.

Discussion for Home page

D M BAPPY — Fri, 15 Apr 2016 06:51:41 -0000

hello

did you use 2D or 3D projections?
have you normalized the final output?
if possible than share the sinogram.mat file, than I can try to reproduce the output.

Discussion for Home page

Sidnei Paciornik — Wed, 13 Apr 2016 21:37:40 -0000

Responses:
1 and 2 - Here is the Matlab code we wrote:
i = 1;
I = imread([proj_dir, sample, '0001', '.tif']);
nstr = '0000';
incremento = floor(proj_tot/(proj_count-1))-1;
sinoI = zeros(size(I,1),size(I,2),proj_count,'double');
sinoI(:,:,1) = im2double(I);
for j=2:proj_count

i = i + incremento;

if i < 10
    nstr = ['000',int2str(i)];
else if i < 100
        nstr = ['00',int2str(i)];
    else if i < 1000
            nstr = ['0',int2str(i)];
        else nstr = int2str(i);
        end
    end
end

I = imread([proj_dir, sample, nstr, '.tif']);
sinoI(:,:,j) = im2double(I);

end;

sinogram = permute(sinoI,[1 3 2]);

3 - Yes, but it didn't seem to affect results.

4 - 100 projections

5 - We did recheck these values ( (12.0159 mm e 5.7462 mm, respectively)

Thank you!

Discussion for Home page

D M BAPPY — Wed, 13 Apr 2016 02:30:14 -0000

I have some more questions
1.how did you create the 'sinogram.mat' file.
2.did you use your own function or matlab built in function?
3.did you try using increasing number of projections?
4.how many projections you have inside your 'sinogram.mat' file
5.recheck and confirm the values of (source_origin and origin_det) variables.

Discussion for Home page

Sidnei Paciornik — Tue, 12 Apr 2016 19:35:11 -0000

We acquired a set of 3200 projections in our Versa 510 MicroCT. We then selected an equally spaced (angular) subset of 100 projections. We used a Matlab routine to load and process. The routine is attached. Any help will be welcome! Thank you!

Discussion for Home page

D M BAPPY — Tue, 12 Apr 2016 02:15:03 -0000

may i know that how did you use a set of projections images?

Discussion for Home page

Sidnei Paciornik — Mon, 11 Apr 2016 17:29:19 -0000

Hello

I am a professor at PUC-Rio university in Brazil. We are trying to use the Astra Toolbox to speed up tomography reconstruction and segmentation with the SIRT algorithm.
We have been able to make the code (SIRT3D_CUDA) run with a subset of projection images we obtained with our Zeiss XRadia Versa 510. However the resulting reconstructed and segmented images are almost totally black with a few bright points that do not seem to relate to the sample.

Any hints? Thank you very much!

Sidnei Paciornik
Associate Professor
Digital Microscopy and Image Processing Lab
DEQM PUC-Rio

Home modified by Willem Jan Palenstijn

Willem Jan Palenstijn — Wed, 23 Dec 2015 12:53:40 -0000

--- v22
+++ v23
@@ -2,7 +2,14 @@

 ## News

-* 2015-05-29: New version 1.6 released. The Python interface developed by Daniel Pelt, and the Matlab Spot toolbox operator wrapping ASTRA developed by Folkert Bleichrodt are now integrated into the main ASTRA Toolbox source tree.
+* 2015-12-23: New version **1.7.1beta** released. This is a small bugfix release after v1.7beta. ASTRA version 1.7beta contains a few large experimental new features, which is why we have given it the beta tag.
+If it does not work properly for you, all files for astra-1.6 are also still available for download: astra-1.6 downloads. New features:
+    * Experimental MPI distributed computing support in Python. This is only available for Linux+Python, as a separate source download (astra-1.7.1beta_MPI.tar. bz2), or the mpi branch on github.
+    * Experimental support in Python for FP and BP of objects composited from multiple 3d data objects, at possibly different resolutions. This also removes some restrictions on data size for 3D GPU FP and BP.
+    * Reduced restrictions on volume geometries: The volume no longer has to be centered, and voxels still have to be cubes, but no longer 1x1x1.
+
+
+* 2015-05-29: New version **1.6** released. The Python interface developed by Daniel Pelt, and the Matlab Spot toolbox operator wrapping ASTRA developed by Folkert Bleichrodt are now integrated into the main ASTRA Toolbox source tree.

 * 2015-01-17: From 25 to 27 March, 2015, iMinds-Vision Lab organizes the second ASTRA Toolbox training session. For more info, please contact Wim Van Aarle: wim.vanaarle@uantwerpen.be.

Home modified by Willem Jan Palenstijn

Willem Jan Palenstijn — Wed, 23 Dec 2015 12:40:50 -0000

--- v21
+++ v22
@@ -24,18 +24,20 @@

 Main downloads:

-* ASTRA v1.6 for Windows 64 bit CUDA/MATLAB: [astra-1.6-matlab-win-x64.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.6/astra-1.6-matlab-win-x64.zip/download)
+* ASTRA v1.7.1beta for Windows 64 bit CUDA/MATLAB: [astra-1.7.1beta-matlab-win-x64.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta-matlab-win-x64.zip/download)

-* ASTRA v1.6 for Windows 64 bit CUDA/Python 2.7: [astra-1.6-python27-win-x64.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.6/astra-1.6-python27-win-x64.zip/download)
+* ASTRA v1.7.1beta for Windows 64 bit CUDA/Python 2.7: [astra-1.7.1beta-python27-win-x64.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta-python27-win-x64.zip/download)

-* ASTRA v1.6 for Windows 64 bit CUDA/Python 3.4: [astra-1.6-python34-win-x64.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.6/astra-1.6-python34-win-x64.zip/download)
+* ASTRA v1.7.1beta for Windows 64 bit CUDA/Python 3.4: [astra-1.7.1beta-python34-win-x64.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta-python34-win-x64.zip/download)

-* ASTRA v1.6 Source Code for Linux: [astra-1.6.tar.bz2](http://sourceforge.net/projects/astra-toolbox/files/astra-1.6/astra-1.6.tar.bz2/download)
+* ASTRA v1.7.1beta Source Code for Linux: [astra-1.7.1beta.tar.bz2](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta.tar.bz2/download)
+
+* ASTRA v1.7.1beta Source Code for Linux, with MPI support: [astra-1.7.1beta_MPI.tar.bz2](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta_MPI.tar.bz2/download)

 For compiling on Windows we only provide Visual Studio 2008 and 2012 project files. We have also packaged a set of external libraries and headers for all the build dependencies:

-* ASTRA v1.6 Source Code for Windows/VS2008/2012: [astra-1.6.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.6/astra-1.6.zip/download)
-* ASTRA v1.6 Compilation Support files for Windows/VS2008/2012: [astra-1.6-windows_build_support.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.6/astra-1.6-windows_build_support.zip/download)
+* ASTRA v1.7.1beta Source Code for Windows/VS2008/2012: [astra-1.7.1beta.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta.zip/download)
+* ASTRA v1.7.1beta Compilation Support files for Windows/VS2008/2012: [astra-1.7.1beta-windows_build_support.zip](http://sourceforge.net/projects/astra-toolbox/files/astra-1.7.1beta/astra-1.7.1beta-windows_build_support.zip/download)